def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if not os.path.exists(opts.output_path):
os.makedirs(opts.output_path)
maker = RarefactionMaker(opts.input_path, opts.depth, opts.depth, 1, opts.num_reps)
maker.rarefy_to_files(
opts.output_path, False, include_lineages=opts.lineages_included, empty_otus_removed=(not opts.keep_empty_otus)
)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if not os.path.exists(opts.output_path):
os.makedirs(opts.output_path)
maker = RarefactionMaker(opts.input_path, opts.depth, opts.depth,
1, opts.num_reps)
maker.rarefy_to_files(opts.output_path, False,
include_lineages=opts.lineages_included,
empty_otus_removed=(not opts.keep_empty_otus))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.step <= 0:
option_parser.error("nonpositive step not allowed (%s was supplied)" % \
(opts.step,))
create_dir(opts.output_path, fail_on_exist=False)
maker = RarefactionMaker(opts.input_path, opts.min, opts.max,
opts.step, opts.num_reps)
maker.rarefy_to_files(opts.output_path, False,
include_lineages=opts.lineages_included,
empty_otus_removed=(not opts.keep_empty_otus))
def test_rarefy_to_files(self):
"""rarefy_to_files should write valid files
"""
maker = RarefactionMaker(self.otu_table_fp, 1, 2, 1, 1)
maker.rarefy_to_files(self.rare_dir,
include_full=True,
include_lineages=False)
fname = os.path.join(self.rare_dir, "rarefaction_1_0.biom")
otu_table = load_table(fname)
self.assertItemsEqual(otu_table.ids(), self.otu_table.ids()[:2])
def test_rarefy_to_files(self):
"""rarefy_to_files should write valid files
"""
maker = RarefactionMaker(self.otu_table_fp, 0, 1, 1, 1)
maker.rarefy_to_files(self.rare_dir,include_full=True,include_lineages=False)
fname = os.path.join(self.rare_dir,"rarefaction_1_0.biom")
otu_table = parse_biom_table(open(fname,'U'))
self.assertFloatEqual(otu_table.SampleIds, self.otu_table.SampleIds[:2])
# third sample had 0 seqs, so it's gone
self.assertFloatEqual(otu_table.ObservationIds, self.otu_table.ObservationIds)
def test_rarefy_to_files2(self):
"""rarefy_to_files should write valid files with some metadata on otus
"""
maker = RarefactionMaker(self.otu_table_meta_fp, 0, 1, 1, 1)
maker.rarefy_to_files(self.rare_dir,
include_full=True,
include_lineages=False)
fname = os.path.join(self.rare_dir, "rarefaction_1_0.biom")
with biom_open(fname, 'U') as biom_file:
otu_table = Table.from_hdf5(biom_file)
self.assertItemsEqual(otu_table.ids(), self.otu_table.ids()[:2])
def test_rarefy_to_files(self):
"""rarefy_to_files should write valid files
"""
maker = RarefactionMaker(self.otu_table_fp, 1, 2, 1, 1)
maker.rarefy_to_files(
self.rare_dir,
include_full=True,
include_lineages=False)
fname = os.path.join(self.rare_dir, "rarefaction_1_0.biom")
otu_table = load_table(fname)
self.assertItemsEqual(
otu_table.ids(),
self.otu_table.ids()[:2])
def test_rarefy_to_files2(self):
"""rarefy_to_files should write valid files with some metadata on otus
"""
maker = RarefactionMaker(self.otu_table_meta_fp, 0, 1, 1, 1)
maker.rarefy_to_files(self.rare_dir,
include_full=True,
include_lineages=False)
fname = os.path.join(self.rare_dir, "rarefaction_1_0.biom")
otu_table = parse_biom_table(open(fname, 'U'))
self.assertItemsEqual(otu_table.SampleIds,
self.otu_table.SampleIds[:2])
# third sample had 0 seqs, so it's gone
self.assertItemsEqual(otu_table.ObservationIds,
self.otu_table.ObservationIds)
def test_rarefy_to_files(self):
"""rarefy_to_files should write valid files
"""
maker = RarefactionMaker(self.otu_table_fp, 0, 1, 1, 1)
maker.rarefy_to_files(
self.rare_dir,
include_full=True,
include_lineages=False)
fname = os.path.join(self.rare_dir, "rarefaction_1_0.biom")
with biom_open(fname, 'U') as biom_file:
otu_table = Table.from_hdf5(biom_file)
self.assertItemsEqual(
otu_table.sample_ids,
self.otu_table.sample_ids[:2])
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.step <= 0:
option_parser.error("step must be greater than 0")
create_dir(opts.output_path, fail_on_exist=False)
maker = RarefactionMaker(opts.input_path, opts.min, opts.max,
opts.step, opts.num_reps)
if opts.subsample_multinomial:
subsample_f = partial(subsample, replace=True)
else:
subsample_f = subsample
maker.rarefy_to_files(opts.output_path,
False,
include_lineages=opts.lineages_included,
empty_otus_removed=(not opts.keep_empty_otus),
subsample_f=subsample_f)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.step <= 0:
option_parser.error("nonpositive step not allowed (%s was supplied)" %
(opts.step, ))
create_dir(opts.output_path, fail_on_exist=False)
maker = RarefactionMaker(opts.input_path, opts.min, opts.max, opts.step,
opts.num_reps)
if opts.subsample_multinomial:
subsample_f = partial(subsample, replace=True)
else:
subsample_f = subsample
maker.rarefy_to_files(opts.output_path,
False,
include_lineages=opts.lineages_included,
empty_otus_removed=(not opts.keep_empty_otus),
subsample_f=subsample_f)
